DESCRIPTION

Generic, context neutral mapper to provide coordinate transforms between two disjoint coordinate systems. It brings into Bioperl the functionality from Ewan Birney's Bio::EnsEMBL::Mapper ported into current bioperl.

This class is aimed for representing mapping between whole chromosomes and contigs, or between contigs and clones, or between sequencing reads and assembly. The submaps are automatically sorted, so they can be added in any order.

To map coordinates to the other direction, you have to swap() the collection. Keeping track of the direction and ID restrictions are left to the calling code.

swap

test

Title : test
Usage : $obj->test;
Function: test that both components of all pairs are of the same length.
Ran automatically.
Example :
Returns : boolean
Args :

map

Title : map
Usage : $newpos = $obj->map($pos);
Function: Map the location from the input coordinate system
to a new value in the output coordinate system.
Example :
Returns : new value in the output coordinate system
Args : integer

_map

Title : _map
Usage : $newpos = $obj->_map($simpleloc);
Function: Internal method that does the actual mapping. Called multiple times
by map() if the location to be mapped is a split location
Example :
Returns : new location in the output coordinate system or undef
Args : Bio::Location::Simple